Variant report

Variant	rs4941677
Chromosome Location	chr13:51490196-51490197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:51481922..51486486-chr13:51489921..51494512,7	MCF-7	breast:
2	chr13:51483191..51486510-chr13:51488472..51491289,4	MCF-7	breast:
3	chr13:51488225..51491111-chr13:51497807..51500675,3	K562	blood:
4	chr13:51488232..51490526-chr13:51522667..51525148,2	MCF-7	breast:
5	chr13:51486556..51488218-chr13:51489286..51491989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233672	Chromatin interaction
ENSG00000136104	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17074987	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274069	0.91[ASN][1000 genomes]
rs4941678	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4942943	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59310144	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561599	0.84[ASN][1000 genomes]
rs6561601	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6561602	0.89[ASN][1000 genomes]
rs6561603	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7316955	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7321027	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7324232	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7988945	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535523	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535526	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535534	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900077	chr13:51446114-51514831	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4941677	RNASEH2B	cis	Artery Tibial	GTEx
rs4941677	RNASEH2B	cis	Muscle Skeletal	GTEx
rs4941677	RNASEH2B	cis	Thyroid	GTEx
rs4941677	RNASEH2B	cis	Esophagus Muscularis	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51485000-51490800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:51485000-51490800	Weak transcription	Lung	lung
3	chr13:51485000-51491200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:51485000-51496200	Weak transcription	Ovary	ovary
5	chr13:51485200-51495600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr13:51485400-51504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr13:51485600-51490600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:51485800-51490800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr13:51486000-51495800	Weak transcription	Fetal Brain Female	brain
10	chr13:51486200-51490800	Enhancers	Primary hematopoietic stem cells	blood
11	chr13:51486400-51490600	Weak transcription	HUVEC	blood vessel
12	chr13:51486400-51490800	Enhancers	Primary B cells from cord blood	blood
13	chr13:51486400-51491000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr13:51486400-51491400	Weak transcription	Brain Substantia Nigra	brain
15	chr13:51486400-51491600	Transcr. at gene 5' and 3'	Dnd41	blood
16	chr13:51486600-51491000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr13:51486600-51491000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr13:51486600-51491200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:51486600-51528400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr13:51486800-51490400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr13:51486800-51490600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:51486800-51490800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr13:51486800-51490800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr13:51486800-51490800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr13:51486800-51490800	Weak transcription	Brain Anterior Caudate	brain
26	chr13:51486800-51491000	Weak transcription	Fetal Muscle Leg	muscle
27	chr13:51486800-51491200	Weak transcription	Liver	Liver
28	chr13:51486800-51491400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr13:51486800-51491600	Weak transcription	HepG2	liver
30	chr13:51486800-51491800	Weak transcription	Brain Angular Gyrus	brain
31	chr13:51486800-51495600	Weak transcription	Fetal Intestine Small	intestine
32	chr13:51487000-51498400	Weak transcription	Fetal Stomach	stomach
33	chr13:51487200-51490800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr13:51487400-51490600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr13:51487400-51493800	Genic enhancers	Fetal Thymus	thymus
36	chr13:51487800-51490600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr13:51488200-51490200	Flanking Active TSS	GM12878-XiMat	blood
38	chr13:51488200-51490400	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr13:51488400-51491000	Enhancers	Primary B cells from peripheral blood	blood
40	chr13:51488400-51491200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr13:51488400-51491600	Enhancers	K562	blood
42	chr13:51488400-51492200	Enhancers	Primary T cells fromperipheralblood	blood
43	chr13:51488400-51492200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr13:51488400-51494600	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr13:51488400-51496200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr13:51488600-51490200	Enhancers	Colon Smooth Muscle	Colon
47	chr13:51488600-51490200	Enhancers	Placenta	Placenta
48	chr13:51488600-51490200	Enhancers	Right Atrium	heart
49	chr13:51488600-51490800	Enhancers	Primary T cells from cord blood	blood
50	chr13:51488600-51490800	Enhancers	Primary T helper cells PMA-I stimulated	--

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